The alloreactive T cell repertoire has been analyzed for the influence of non-MHC determinants on alloreactivity. The responses of cloned T cells to Mlsa were analyzed in clones generated specifically to Mlsa stimulator cells as well as in clones specific for soluble antigens (antigen specific), foreign I region products (alloreactive), or syngeneic I products (autoreactive) which showed cross reactive recognition of Mlsa. It is demonstrated through the use of congenic strains, recombinant inbred strains, and monoclonal antibodies, that cloned T cell responses were specific for Mls and that this recognition was MHC restricted. The overall importance of non-MHC encoded determinants in alloreactive T cell recognition was surveyed by examining a panel of 70 antigen specific and/or autoreactive T cell clones for coincidental alloreactivity. Approximately 80% of the clones analyzed revealed one or more alloantigen specific cross-reactivities. In several of these instances, specificity appeared to be for MHC products alone, without detectable influence of non-MHC genes. However, in the majority of instances, alloreactive specificity involved non-MHC as wells MHC gene products expressed by stimulating populations. These findings therefore suggest that the high frequency of alloreactive T cells observed in multiple experimental systems may reflect a frequent role of non-MHC as well as MHC encoded gene products. The cytotoxic T cell repertoire specific for class I allogeneic and xenogeneic determinants was studied. Through the use of radiation bone marrow chimeras, it was demonstrated that responsiveness to Kb mutant determinants was the outcome of unique interactions between both T cell genotype and maturation environment. Through the use of a transgenic mouse model, in which porcine class I genes had been introduced into the germ line of murine cells, it was demonstrated that normal murine T cells expressed a cytotoxic T cell repertoire specific for xenogeneic class I determinants expressed on mouse cells. This repertoire was cross-reactive with the alloreactive cytotoxic T cell repertoire.